def CreatePDB(self, coordArray, fPath, ofile):
sloppyparser = PDBParser(PERMISSIVE=True, QUIET=True)
structure = sloppyparser.get_structure("MD_system", fPath)
print("\nGenerating PDB file...")
sb = StructureBuilder()
sb.set_header(structure.header)
# Iterate through models
for i in range(len(list(structure.get_models()))):
# Iterate through chains
models = list(structure.get_models())
counter = 0
for j in range(len(list(models[i].get_chains()))):
chains = list(models[i].get_chains())
#Iterate thgouth residues
for k in range(len(list(chains[j].get_residues()))):
#Iterate through
residues = list(chains[j].get_residues())
for l in range(len(list(residues[k].get_atoms()))):
#Set coord for each
for atom in structure[i][chains[j].id][
residues[k].id].get_atoms():
structure[i][chains[j].id][residues[k].id][
atom.id].set_coord(
np.array((float(coordArray[counter][0]),
float(coordArray[counter][1]),
float(coordArray[counter][2]))))
#print(structure[i][chains[j].id][residues[k].id][atom.id].get_vector())
counter += 1
io = PDBIO()
io.set_structure(structure)
io.save(ofile)
print("Transform file written to: " + ofile)
def init_structure(
self,
total_num_bonds,
total_num_atoms,
total_num_groups,
total_num_chains,
total_num_models,
structure_id,
):
"""Initialize the structure object.
:param total_num_bonds: the number of bonds in the structure
:param total_num_atoms: the number of atoms in the structure
:param total_num_groups: the number of groups in the structure
:param total_num_chains: the number of chains in the structure
:param total_num_models: the number of models in the structure
:param structure_id: the id of the structure (e.g. PDB id)
"""
self.structure_builder = StructureBuilder()
self.structure_builder.init_structure(structure_id=structure_id)
self.chain_index_to_type_map = {}
self.chain_index_to_seq_map = {}
self.chain_index_to_description_map = {}
self.chain_counter = 0
def __init__(self, structure_builder=None, QUIET=False):
"""Create a FastMMCIFParser object.
The mmCIF parser calls a number of standard methods in an aggregated
StructureBuilder object. Normally this object is instanciated by the
parser object itself, but if the user provides his/her own
StructureBuilder object, the latter is used instead.
The main difference between this class and the regular MMCIFParser is
that only 'ATOM' and 'HETATM' lines are parsed here. Use if you are
interested only in coordinate information.
Arguments:
- structure_builder - an optional user implemented StructureBuilder class.
- QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
the SMCRA data will be suppressed. If false (DEFAULT), they will be shown.
These warnings might be indicative of problems in the mmCIF file!
"""
if structure_builder is not None:
self._structure_builder = structure_builder
else:
self._structure_builder = StructureBuilder()
self.line_counter = 0
self.build_structure = None
self.QUIET = bool(QUIET)
def read_mmcif_to_biopython(path):
"""Read in mmcif protein structure and report its Biopython structure
Args:
path (str): Path to the mmcif file.
Raises:
ValueError: In case _atom_site table is not present in the file.
Returns:
Bio.PDB.Structure.Structure: BioPython PDB structure
"""
if not os.path.isfile(path):
raise IOError("File {} not found".format(path))
structure_builder = StructureBuilder()
parsed = MMCIF2Dict().parse(path)
file_name = os.path.basename(path).split(".")[0]
structure_id = next((x for x in parsed), file_name).lower()
structure_builder.init_structure(structure_id)
try:
perceived_atom_site = list(parsed.values())[0]["_atom_site"]
_atom_site = _trim_models(perceived_atom_site)
_parse_atom_site_biopython(_atom_site, structure_builder)
except KeyError:
raise ValueError("The cif file does not contain _atom_site record")
return structure_builder.get_structure()
def __init__(self,
PERMISSIVE=True,
get_header=False,
structure_builder=None,
QUIET=False):
"""Create a PDBParser object.
The PDB parser call a number of standard methods in an aggregated
StructureBuilder object. Normally this object is instanciated by the
PDBParser object itself, but if the user provides his/her own
StructureBuilder object, the latter is used instead.
Arguments:
- PERMISSIVE - Evaluated as a Boolean. If false, exceptions in
constructing the SMCRA data structure are fatal. If true (DEFAULT),
the exceptions are caught, but some residues or atoms will be missing.
THESE EXCEPTIONS ARE DUE TO PROBLEMS IN THE PDB FILE!.
- get_header - unused argument kept for historical compatibilty.
- structure_builder - an optional user implemented StructureBuilder class.
- QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
the SMCRA data will be suppressed. If false (DEFAULT), they will be shown.
These warnings might be indicative of problems in the PDB file!
"""
# get_header is not used but is left in for API compatibility
if structure_builder is not None:
self.structure_builder = structure_builder
else:
self.structure_builder = StructureBuilder()
self.header = None
self.trailer = None
self.line_counter = 0
self.PERMISSIVE = bool(PERMISSIVE)
self.QUIET = bool(QUIET)
def __init__(self, structure_builder=None):
# get_header is not used but is left in for API compatibility
if structure_builder is not None:
self.structure_builder = structure_builder
else:
self.structure_builder = StructureBuilder()
self.header = None
self.line_counter = 0
def build_structure(atoms):
sb = StructureBuilder()
sb.init_structure('pdb')
sb.init_seg(' ')
sb.init_model(0)
sb.init_chain('A')
i = 1
for atom in atoms:
sb.init_residue('DUM', ' ', i, ' ')
sb.structure[0]['A'].child_list[i - 1].add(atom)
i += 1
return sb.structure
def set_structure(self, pdb_object):
"""Check what the user is providing and build a structure."""
# The idea here is to build missing upstream components of
# the SMCRA object representation. E.g., if the user provides
# a Residue, build Structure/Model/Chain.
if pdb_object.level == "S":
structure = pdb_object
else: # Not a Structure
sb = StructureBuilder()
sb.init_structure("pdb")
sb.init_seg(" ")
if pdb_object.level == "M":
sb.structure.add(pdb_object.copy())
self.structure = sb.structure
else: # Not a Model
sb.init_model(0)
if pdb_object.level == "C":
sb.structure[0].add(pdb_object.copy())
else: # Not a Chain
chain_id = "A" # default
sb.init_chain(chain_id)
if pdb_object.level == "R": # Residue
# Residue extracted from a larger structure?
if pdb_object.parent is not None:
og_chain_id = pdb_object.parent.id
sb.structure[0][chain_id].id = og_chain_id
chain_id = og_chain_id
sb.structure[0][chain_id].add(pdb_object.copy())
else: # Atom
sb.init_residue("DUM", " ", 1, " ") # Dummy residue
sb.structure[0][chain_id].child_list[0].add(
pdb_object.copy())
# Fix chain identifier if Atom has grandparents.
try:
og_chain_id = pdb_object.parent.parent.id
except AttributeError: # pdb_object.parent == None
pass
else:
sb.structure[0][chain_id].id = og_chain_id
# Return structure
structure = sb.structure
self.structure = structure
def pdb_writer(graph, results, dir_name="templates"):
PDB_CODE = graph.protein_name
structure = graph.structure
path = "%s/%s/" % (dir_name, PDB_CODE)
if len(results) > 0:
if not os.path.exists(path):
os.makedirs(path)
else:
print 'No results'
return
top = min(NUM_OF_RESULTS_TO_SAVE, len(results))
i = 0
for key, value in results[:top]:
# TODO - save as different chains
sb = StructureBuilder()
sb.init_structure(PDB_CODE)
sb.init_model(0)
sb.init_chain('X')
for node_id in key[0]:
for res in graph.nodes[node_id].residues:
sb.init_seg(res.get_segid())
sb.init_residue(res.get_resname(),
res.get_id()[0],
res.get_id()[1],
res.get_id()[2])
for atom in res:
sb.init_atom(atom.get_name(), atom.get_coord(),
atom.get_bfactor(), atom.get_occupancy(),
atom.get_altloc(), atom.get_fullname())
sb.init_chain('Y')
for node_id in key[1]:
for res in graph.nodes[node_id].residues:
sb.init_residue(res.get_resname(),
res.get_id()[0],
res.get_id()[1],
res.get_id()[2])
for atom in res:
sb.init_atom(atom.get_name(), atom.get_coord(),
atom.get_bfactor(), atom.get_occupancy(),
atom.get_altloc(), atom.get_fullname())
filename = path + "interface%d.pdb" % (i)
io = PDBIO()
io.set_structure(sb.get_structure())
io.save(filename)
i += 1
return 1
def coarse_grain(self, cg_type="CA_TRACE"):
"""
Reduces the protein structure complexity to a few (pseudo-)atoms per residue.
Parameters:
- cg_type: CA_TRACE (Ca-only) [Default]
ENCAD_3P (CA, O, SC Beads)
MARTINI (CA, O, SC Beads)
Returns a new structure object.
"""
# Import CG Types
import CG_Models
CG_Library = {
"CA_TRACE": CG_Models.CA_TRACE,
"ENCAD_3P": CG_Models.ENCAD_3P,
"MARTINI": CG_Models.MARTINI
}
CG_Method = CG_Library[cg_type]
# Creates a brand new structure object
from Bio.PDB.StructureBuilder import StructureBuilder
structure_builder = StructureBuilder()
cg_id = "CG_" + self.id
structure_builder.init_structure(cg_id)
structure_builder.init_seg(' ') # Empty SEGID
for model in self:
structure_builder.init_model(model.id)
for chain in model:
structure_builder.init_chain(chain.id)
cur_chain = structure_builder.chain
for residue in chain:
cg_residue = CG_Method(residue)
cur_chain.add(cg_residue)
cg_structure = structure_builder.get_structure()
return cg_structure
def write_helical_axes(self, filename):
"""Writes helical axes in PDB format."""
sb = StructureBuilder()
sb.init_structure('')
sb.init_model('')
for cpos, chain in enumerate(self.chains):
sb.init_chain(str(cpos))
sb.init_seg('')
for pos, i in enumerate(chain.res[1:-1]):
sb.init_residue('ALA', ' ', pos, ' ')
sb.init_atom('CA', i.O._ar, 0, 0, " ", ' CA ', 1)
io = PDBIO()
io.set_structure(sb.structure)
io.save(filename)
def __init__(self,
get_header=False,
structure_builder=None,
PERMISSIVE=True):
"""arguments:
PERMISSIVE, Evaluated as a Boolean. If ture, the exception are caught,
some residues or atoms will be missing.THESE EXCEPTIONS ARE DUE TO PROBLEMS IN THE PDB FILE!
structure_builder, an optional user implemented StructureBuilder class.
"""
#get a structure_builder class
if structure_builder is not None:
self.structure_builder = structure_builder
else:
self.structure_builder = StructureBuilder()
self.header = None
self.trailer = None
self.line_counter = 0
self.PERMISSIVE = bool(PERMISSIVE)
def __init__(self,
structure_builder=None,
auth_chains=True,
auth_residues=True,
QUIET=False):
"""Create a FastMMCIFParser object.
The mmCIF parser calls a number of standard methods in an aggregated
StructureBuilder object. Normally this object is instantiated by the
parser object itself, but if the user provides his/her own
StructureBuilder object, the latter is used instead.
The main difference between this class and the regular MMCIFParser is
that only 'ATOM' and 'HETATM' lines are parsed here. Use if you are
interested only in coordinate information.
Arguments:
- structure_builder - an optional user implemented StructureBuilder class.
- auth_chains - True by default. If true, use the author chain IDs.
If false, use the re-assigned mmCIF chain IDs.
- auth_residues - True by default. If true, use the author residue numbering.
If false, use the mmCIF "label" residue numbering, which has no insertion
codes, and strictly increments residue numbers.
NOTE: Non-polymers such as water don't have a "label" residue number,
and will be skipped.
- QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
the SMCRA data will be suppressed. If false (DEFAULT), they will be shown.
These warnings might be indicative of problems in the mmCIF file!
"""
if structure_builder is not None:
self._structure_builder = structure_builder
else:
self._structure_builder = StructureBuilder()
self.line_counter = 0
self.build_structure = None
self.auth_chains = bool(auth_chains)
self.auth_residues = bool(auth_residues)
self.QUIET = bool(QUIET)
def __init__(self, structure_builder=None, QUIET=False):
"""Create a PDBParser object.
The PDB parser call a number of standard methods in an aggregated
StructureBuilder object. Normally this object is instanciated by the
MMCIParser object itself, but if the user provides his/her own
StructureBuilder object, the latter is used instead.
Arguments:
- structure_builder - an optional user implemented StructureBuilder class.
- QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
the SMCRA data will be suppressed. If false (DEFAULT), they will be shown.
These warnings might be indicative of problems in the PDB file!
"""
if structure_builder is not None:
self._structure_builder = structure_builder
else:
self._structure_builder = StructureBuilder()
# self.header = None
# self.trailer = None
self.line_counter = 0
self.build_structure = None
self.QUIET = bool(QUIET)
def __init__(self, PERMISSIVE=1, get_header=0, structure_builder=None):
"""
The PDB parser call a number of standard methods in an aggregated
StructureBuilder object. Normally this object is instanciated by the
PDBParser object itself, but if the user provides his own StructureBuilder
object, the latter is used instead.
Arguments:
o PERMISSIVE - int, if this is 0 exceptions in constructing the
SMCRA data structure are fatal. If 1 (DEFAULT), the exceptions are
caught, but some residues or atoms will be missing. THESE EXCEPTIONS
ARE DUE TO PROBLEMS IN THE PDB FILE!.
o structure_builder - an optional user implemented StructureBuilder class.
"""
if structure_builder!=None:
self.structure_builder=structure_builder
else:
self.structure_builder=StructureBuilder()
self.header=None
self.trailer=None
self.line_counter=0
self.PERMISSIVE=PERMISSIVE
def set_structure(self, pdb_object):
"""Check what the user is providing and build a structure."""
if pdb_object.level == "S":
structure = pdb_object
else:
sb = StructureBuilder()
sb.init_structure("pdb")
sb.init_seg(" ")
# Build parts as necessary
if pdb_object.level == "M":
sb.structure.add(pdb_object.copy())
self.structure = sb.structure
else:
sb.init_model(0)
if pdb_object.level == "C":
sb.structure[0].add(pdb_object.copy())
else:
sb.init_chain("A")
if pdb_object.level == "R":
try:
parent_id = pdb_object.parent.id
sb.structure[0]["A"].id = parent_id
except Exception:
pass
sb.structure[0]["A"].add(pdb_object.copy())
else:
# Atom
sb.init_residue("DUM", " ", 1, " ")
try:
parent_id = pdb_object.parent.parent.id
sb.structure[0]["A"].id = parent_id
except Exception:
pass
sb.structure[0]["A"].child_list[0].add(
pdb_object.copy())
# Return structure
structure = sb.structure
self.structure = structure
def set_structure(self, pdb_object):
"""Check what object the user is providing and build a structure."""
# This is duplicated from the PDBIO class
if pdb_object.level == "S":
structure = pdb_object
else:
sb = StructureBuilder()
sb.init_structure('pdb')
sb.init_seg(' ')
# Build parts as necessary
if pdb_object.level == "M":
sb.structure.add(pdb_object)
self.structure = sb.structure
else:
sb.init_model(0)
if pdb_object.level == "C":
sb.structure[0].add(pdb_object)
else:
sb.init_chain('A')
if pdb_object.level == "R":
try:
parent_id = pdb_object.parent.id
sb.structure[0]['A'].id = parent_id
except ValueError:
pass
sb.structure[0]['A'].add(pdb_object)
else:
# Atom
sb.init_residue('DUM', ' ', 1, ' ')
try:
parent_id = pdb_object.parent.parent.id
sb.structure[0]['A'].id = parent_id
except ValueError:
pass
sb.structure[0]['A'].child_list[0].add(pdb_object)
# Return structure
structure = sb.structure
self.structure = structure
def set_structure(self, pdb_object):
# Check what the user is providing and build a structure appropriately
if pdb_object.level == "S":
structure = pdb_object
else:
sb = StructureBuilder()
sb.init_structure('pdb')
sb.init_seg(' ')
# Build parts as necessary
if pdb_object.level == "M":
sb.structure.add(pdb_object)
self.structure = sb.structure
else:
sb.init_model(0)
if pdb_object.level == "C":
sb.structure[0].add(pdb_object)
else:
sb.init_chain('A')
if pdb_object.level == "R":
try:
parent_id = pdb_object.parent.id
sb.structure[0]['A'].id = parent_id
except Exception:
pass
sb.structure[0]['A'].add(pdb_object)
else:
# Atom
sb.init_residue('DUM', ' ', 1, ' ')
try:
parent_id = pdb_object.parent.parent.id
sb.structure[0]['A'].id = parent_id
except Exception:
pass
sb.structure[0]['A'].child_list[0].add(pdb_object)
# Return structure
structure = sb.structure
self.structure = structure
def __init__(self, PERMISSIVE=1, structure_builder=None):
if structure_builder != None:
self.structure_builder = structure_builder
else:
self.structure_builder = StructureBuilder()
self.PERMISSIVE = PERMISSIVE
def read_PIC(file: TextIO, verbose: bool = False) -> Structure:
"""Load Protein Internal Coordinate (.pic) data from file.
PIC file format:
- comment lines start with #
- (optional) PDB HEADER record
- idcode and deposition date recommended but optional
- deposition date in PDB format or as changed by Biopython
- (optional) PDB TITLE record
- repeat:
- Biopython Residue Full ID - sets residue IDs of returned structure
- (optional) PDB N, CA, C ATOM records for chain start
- (optional) PIC Hedra records for residue
- (optional) PIC Dihedra records for residue
- (optional) BFAC records listing AtomKeys and b-factors
An improvement would define relative positions for HOH (water) entries.
N.B. dihedron (i-1)C-N-CA-CB is ignored in assembly if O exists.
C-beta is by default placed using O-C-CA-CB, but O is missing
in some PDB file residues, which means the sidechain cannot be
placed. The alternate CB path (i-1)C-N-CA-CB is provided to
circumvent this, but if this is needed then it must be adjusted in
conjunction with PHI ((i-1)C-N-CA-C) as they overlap. (i-1)C-N-CA-CB is
included by default in .pic files for consistency and informational
(e.g. statistics gathering) purposes, as otherwise the dihedron would only
appear in the few cases it is needed for.
:param Bio.File file: file name or handle
:param bool verbose: complain when lines not as expected
:returns: Biopython Structure object, Residues with .internal_coord attributes
but no coordinates except for chain start N, CA, C atoms if supplied,
**OR** None on parse fail (silent unless verbose=True)
"""
pdb_hdr_re = re.compile(
r"^HEADER\s{4}(?P<cf>.{1,40})"
r"(?:\s+(?P<dd>\d\d\d\d-\d\d-\d\d|\d\d-\w\w\w-\d\d))?"
r"(?:\s+(?P<id>[0-9A-Z]{4}))?\s*$")
# ^\('(?P<pid>\w*)',\s(?P<mdl>\d+),\s'(?P<chn>\w)',\s\('(?P<het>\s|[\w-]+)',\s(?P<pos>\d+),\s'(?P<icode>\s|\w)'\)\)\s(?P<res>[A-Z]{3})\s(\[(?P<segid>[a-zA-z\s]{4})\])?\s*$
pdb_ttl_re = re.compile(r"^TITLE\s{5}(?P<ttl>.+)\s*$")
biop_id_re = re.compile(r"^\('(?P<pid>[^\s]*)',\s(?P<mdl>\d+),\s"
r"'(?P<chn>\s|\w)',\s\('(?P<het>\s|[\w\s-]+)"
r"',\s(?P<pos>-?\d+),\s'(?P<icode>\s|\w)'\)\)"
r"\s+(?P<res>[\w]{1,3})"
r"(\s\[(?P<segid>[a-zA-z\s]+)\])?"
r"\s*$")
pdb_atm_re = re.compile(r"^ATOM\s\s(?:\s*(?P<ser>\d+))\s(?P<atm>[\w\s]{4})"
r"(?P<alc>\w|\s)(?P<res>[\w]{3})\s(?P<chn>.)"
r"(?P<pos>[\s\-\d]{4})(?P<icode>[A-Za-z\s])\s\s\s"
r"(?P<x>[\s\-\d\.]{8})(?P<y>[\s\-\d\.]{8})"
r"(?P<z>[\s\-\d\.]{8})(?P<occ>[\s\d\.]{6})"
r"(?P<tfac>[\s\d\.]{6})\s{6}"
r"(?P<segid>[a-zA-z\s]{4})(?P<elm>.{2})"
r"(?P<chg>.{2})?\s*$")
bfac_re = re.compile(r"^BFAC:\s([^\s]+\s+[\-\d\.]+)"
r"\s*([^\s]+\s+[\-\d\.]+)?"
r"\s*([^\s]+\s+[\-\d\.]+)?"
r"\s*([^\s]+\s+[\-\d\.]+)?"
r"\s*([^\s]+\s+[\-\d\.]+)?")
bfac2_re = re.compile(r"([^\s]+)\s+([\-\d\.]+)")
struct_builder = StructureBuilder()
# init empty header dict
# - could use to parse HEADER and TITLE lines except
# deposition_date format changed from original PDB header
header_dict = _parse_pdb_header_list([])
curr_SMCS = [None, None, None, None] # struct model chain seg
SMCS_init = [
struct_builder.init_structure,
struct_builder.init_model,
struct_builder.init_chain,
struct_builder.init_seg,
]
sb_res = None
with as_handle(file, mode="r") as handle:
for aline in handle.readlines():
if aline.startswith("#"):
pass # skip comment lines
elif aline.startswith("HEADER "):
m = pdb_hdr_re.match(aline)
if m:
header_dict["head"] = m.group("cf") # classification
header_dict["idcode"] = m.group("id")
header_dict["deposition_date"] = m.group("dd")
elif verbose:
print("Reading pic file", file, "HEADER parse fail: ",
aline)
elif aline.startswith("TITLE "):
m = pdb_ttl_re.match(aline)
if m:
header_dict["name"] = m.group("ttl").strip()
# print('TTL: ', m.group('ttl').strip())
elif verbose:
print("Reading pic file", file, "TITLE parse fail:, ",
aline)
elif aline.startswith("("): # Biopython ID line for Residue
m = biop_id_re.match(aline)
if m:
# check SMCS = Structure, Model, Chain, SegID
segid = m.group(9)
if segid is None:
segid = " "
this_SMCS = [
m.group(1),
int(m.group(2)),
m.group(3), segid
]
if curr_SMCS != this_SMCS:
# init new SMCS level as needed
for i in range(4):
if curr_SMCS[i] != this_SMCS[i]:
SMCS_init[i](this_SMCS[i])
curr_SMCS[i] = this_SMCS[i]
if 0 == i:
# 0 = init structure so add header
struct_builder.set_header(header_dict)
elif 1 == i:
# new model means new chain and new segid
curr_SMCS[2] = curr_SMCS[3] = None
struct_builder.init_residue(
m.group("res"),
m.group("het"),
int(m.group("pos")),
m.group("icode"),
)
sb_res = struct_builder.residue
if 2 == sb_res.is_disordered():
for r in sb_res.child_dict.values():
if not r.internal_coord:
sb_res = r
break
sb_res.internal_coord = IC_Residue(sb_res)
# print('res id:', m.groupdict())
# print(report_IC(struct_builder.get_structure()))
else:
if verbose:
print("Reading pic file", file,
"residue ID parse fail: ", aline)
return None
elif aline.startswith("ATOM "):
m = pdb_atm_re.match(aline)
if m:
if sb_res is None:
# ATOM without res spec already loaded, not a pic file
if verbose:
print(
"Reading pic file",
file,
"ATOM without residue configured:, ",
aline,
)
return None
if sb_res.resname != m.group("res") or sb_res.id[1] != int(
m.group("pos")):
if verbose:
print(
"Reading pic file",
file,
"ATOM not in configured residue (",
sb_res.resname,
str(sb_res.id),
"):",
aline,
)
return None
coord = numpy.array(
(float(m.group("x")), float(
m.group("y")), float(m.group("z"))),
"f",
)
struct_builder.init_atom(
m.group("atm").strip(),
coord,
float(m.group("tfac")),
float(m.group("occ")),
m.group("alc"),
m.group("atm"),
int(m.group("ser")),
m.group("elm").strip(),
)
# print('atom: ', m.groupdict())
# elif verbose:
# print("Reading pic file", file, "ATOM parse fail:", aline)
elif aline.startswith("BFAC: "):
m = bfac_re.match(aline)
if m:
for bfac_pair in m.groups():
if bfac_pair is not None:
m2 = bfac2_re.match(bfac_pair)
if m2 and sb_res is not None and sb_res.internal_coord:
rp = sb_res.internal_coord
rp.bfactors[m2.group(1)] = float(m2.group(2))
# else:
# print('Reading pic file', file, 'B-factor line fail: ', aline)
else:
m = Edron.edron_re.match(aline)
if m and sb_res is not None:
sb_res.internal_coord.load_PIC(m.groupdict())
elif m:
print(
"PIC file: ",
file,
" error: no residue info before reading (di/h)edron data: ",
aline,
)
return None
elif aline.strip():
if verbose:
print("Reading PIC file", file, "parse fail on: .",
aline, ".")
return None
struct = struct_builder.get_structure()
for chn in struct.get_chains():
chnp = chn.internal_coord = IC_Chain(chn)
# done in IC_Chain init : chnp.set_residues()
chnp.link_residues()
chnp.init_edra()
# print(report_PIC(struct_builder.get_structure()))
return struct
def get_structure(self, structure_id, filename):
self._mmcif_dict = MMCIF2Dict(filename)
self._structure_builder = StructureBuilder()
self._build_structure(structure_id)
return self._structure_builder.get_structure()
def read_PIC(file):
"""Load Protein Internal Coordinate (PIC) data from file.
PIC file format:
# comment lines start with #
(optional) PDB HEADER record
- idcode and deposition date recommended but optional
- deposition date in PDB format or as changed by Biopython
(optional) PDB TITLE record
repeat:
Biopython Residue Full ID - sets ID of returned structure
(optional) PDB ATOM records for chain start N, CA, C
PIC Hedra records for residue
PIC Dihedra records for residue
:param Bio.File file: file name or handle
:returns: Biopython Structure object, Residues with .pic attributes
but no coordinates except for chain start N, CA, C atoms if supplied,
or None on parse fail (silent, no exception rasied)
"""
pdb_hdr_re = re.compile(
r'^HEADER\s{4}(?P<cf>.{1,40})'
r'(?:\s+(?P<dd>\d\d\d\d-\d\d-\d\d|\d\d-\w\w\w-\d\d))?'
r'(?:\s+(?P<id>[0-9A-Z]{4}))?\s*$', )
# ^\('(?P<pid>\w*)',\s(?P<mdl>\d+),\s'(?P<chn>\w)',\s\('(?P<het>\s|[\w-]+)',\s(?P<pos>\d+),\s'(?P<icode>\s|\w)'\)\)\s(?P<res>[A-Z]{3})\s(\[(?P<segid>[a-zA-z\s]{4})\])?\s*$
pdb_ttl_re = re.compile(r'^TITLE\s{5}(?P<ttl>.+)\s*$')
biop_id_re = re.compile(r"^\('(?P<pid>\w*)',\s(?P<mdl>\d+),\s"
r"'(?P<chn>\s|\w)',\s\('(?P<het>\s|[\w\s-]+)"
r"',\s(?P<pos>-?\d+),\s'(?P<icode>\s|\w)'\)\)"
r'\s+(?P<res>[\w]{1,3})'
r'(\s\[(?P<segid>[a-zA-z\s]+)\])?'
r'\s*$')
pdb_atm_re = re.compile(r'^ATOM\s\s(?:\s*(?P<ser>\d+))\s(?P<atm>[\w\s]{4})'
r'(?P<alc>\w|\s)(?P<res>[\w]{3})\s(?P<chn>.)'
r'(?P<pos>[\s\-\d]{4})(?P<icode>[A-Za-z\s])\s\s\s'
r'(?P<x>[\s\-\d\.]{8})(?P<y>[\s\-\d\.]{8})'
r'(?P<z>[\s\-\d\.]{8})(?P<occ>[\s\d\.]{6})'
r'(?P<tfac>[\s\d\.]{6})\s{6}'
r'(?P<segid>[a-zA-z\s]{4})(?P<elm>.{2})'
r'(?P<chg>.{2})?\s*$')
bfac_re = re.compile(r'^BFAC:\s([^\s]+\s+[\-\d\.]+)'
r'\s*([^\s]+\s+[\-\d\.]+)?'
r'\s*([^\s]+\s+[\-\d\.]+)?'
r'\s*([^\s]+\s+[\-\d\.]+)?'
r'\s*([^\s]+\s+[\-\d\.]+)?')
bfac2_re = re.compile(r'([^\s]+)\s+([\-\d\.]+)')
struct_builder = StructureBuilder()
# init empty header dict
# - could use to parse HEADER and TITLE lines except
# deposition_date format changed from original PDB header
header_dict = _parse_pdb_header_list([])
curr_SMCS = [None, None, None, None] # struct model chain seg
SMCS_init = [
struct_builder.init_structure, struct_builder.init_model,
struct_builder.init_chain, struct_builder.init_seg
]
sb_res = None
with as_handle(file, mode='r') as handle:
for aline in handle.readlines():
if aline.startswith('#'):
pass # skip comment lines
elif aline.startswith('HEADER '):
m = pdb_hdr_re.match(aline)
if m:
header_dict['head'] = m.group('cf') # classification
header_dict['idcode'] = m.group('id')
header_dict['deposition_date'] = m.group('dd')
else:
print('Reading pic file', file, 'HEADER fail: ', aline)
pass
elif aline.startswith('TITLE '):
m = pdb_ttl_re.match(aline)
if m:
header_dict['name'] = m.group('ttl').strip()
# print('TTL: ', m.group('ttl').strip())
else:
print('Reading pic file', file, 'TITLE fail:, ', aline)
elif aline.startswith('('): # Biopython ID line for Residue
m = biop_id_re.match(aline)
if m:
# check SMCS = Structure, Model, Chain, SegID
segid = m.group(9)
if segid is None:
segid = ' '
this_SMCS = [
m.group(1),
int(m.group(2)),
m.group(3), segid
]
if curr_SMCS != this_SMCS:
# init new SMCS level as needed
for i in range(4):
if curr_SMCS[i] != this_SMCS[i]:
SMCS_init[i](this_SMCS[i])
curr_SMCS[i] = this_SMCS[i]
if 0 == i:
# 0 = init structure so add header
struct_builder.set_header(header_dict)
elif 1 == i:
# new model means new chain and new segid
curr_SMCS[2] = curr_SMCS[3] = None
struct_builder.init_residue(m.group('res'), m.group('het'),
int(m.group('pos')),
m.group('icode'))
sb_res = struct_builder.residue
if 2 == sb_res.is_disordered():
for r in sb_res.child_dict.values():
if not hasattr(r, 'internal_coord'):
sb_res = r
break
sb_res.internal_coord = IC_Residue(sb_res)
# print('res id:', m.groupdict())
# print(report_PIC(struct_builder.get_structure()))
else:
print('Reading pic file', file, 'residue fail: ', aline)
elif aline.startswith('ATOM '):
m = pdb_atm_re.match(aline)
if m:
if sb_res is None:
# ATOM without res spec already loaded, not a pic file
print('no sb_res - not pic file', aline)
return None
if (sb_res.resname != m.group('res')
or sb_res.id[1] != int(m.group('pos'))):
# TODO: better exception here?
raise Exception(
'pic ATOM read confusion: %s %s %s' %
(sb_res.resname, str(sb_res.id), aline))
coord = numpy.array(
(float(m.group('x')), float(
m.group('y')), float(m.group('z'))), "f")
struct_builder.init_atom(
m.group('atm').strip(), coord, float(m.group('tfac')),
float(m.group('occ')), m.group('alc'), m.group('atm'),
int(m.group('ser')),
m.group('elm').strip())
# print('atom: ', m.groupdict())
else:
print('Reading pic file', file, 'ATOM fail: ', aline)
elif aline.startswith('BFAC: '):
m = bfac_re.match(aline)
if m:
for bfac_pair in m.groups():
if bfac_pair is not None:
m2 = bfac2_re.match(bfac_pair)
if (m2 and sb_res is not None
and hasattr(sb_res, 'internal_coord')):
rp = sb_res.internal_coord
rp.bfactors[m2.group(1)] = float(m2.group(2))
else:
m = Edron.edron_re.match(aline)
if m:
sb_res.internal_coord.load_PIC(m.groupdict())
elif aline.strip():
print('Reading PIC file', file, 'parse fail on: .', aline,
'.')
return None
struct = struct_builder.get_structure()
for chn in struct.get_chains():
chnp = chn.internal_coord = IC_Chain(chn)
# done in IC_Chain init : chnp.set_residues()
chnp.link_residues()
chnp.render_dihedra()
# print(report_PIC(struct_builder.get_structure()))
return struct
'T': 8, # Turn
'F': 9 # Fibril
}
# Load things
P = PDBParser()
# P = PDBParser()
io = PDBIO()
# Parse PDB and run DSSP
pdbf_path = os.path.abspath(sys.argv[1])
aa_model = P.get_structure('aa_model', pdbf_path)
# Convert to MARTINI types
# Assign by chain and build the cg structure already
structure_builder = StructureBuilder()
structure_builder.init_structure("cg_model")
structure_builder.init_seg(' ') # Empty SEGID
nbeads = 0
for model in aa_model:
structure_builder.init_model(model.id)
dssp = DSSP(model, pdbf_path)
for chain in model:
structure_builder.init_chain(chain.id)
# Get SS information and translate it to MARTINI
dssp_ss = []
def __init__(self, structure_builder=None):
if structure_builder != None:
self.structure_builder = structure_builder
else:
self.structure_builder = StructureBuilder()
def pdb_extract(structure, **kwargs):
# model to extract from pdb
extract_model = None if not 'model' in kwargs else kwargs['model']
new_model_id = -1 if not 'new_model' in kwargs else kwargs['new_model']
extract_chain = None if not 'chain' in kwargs else kwargs['chain']
first_res = None if not 'first_res' in kwargs else kwargs['first_res']
last_res = None if not 'last_res' in kwargs else kwargs['last_res']
new_first_res = None if not 'new_first_res' in kwargs else kwargs[
'new_first_res']
gap_count = 0 if not 'gap_count' in kwargs else kwargs['gap_count']
water_id = None if not 'water' in kwargs else kwargs['water']
model_rebumber_flag = bool((extract_model is not None)
or new_model_id >= 0)
res_renumber_flag = bool(first_res or last_res or new_first_res
or gap_count)
structure_builder = StructureBuilder()
structure_builder.init_structure('pdb_extract')
structure_builder.set_line_counter(0)
line_counter = 0
start_resseq_by_default = 1 if not new_first_res else new_first_res
for model in structure:
if model_rebumber_flag and \
( extract_model is not None ) and model.get_id() != extract_model:
continue
if model_rebumber_flag and new_model_id >= 0:
this_model_id = new_model_id
new_model_id += 1
else:
this_model_id = model.get_id()
structure_builder.init_model(this_model_id, this_model_id)
for chain in model:
if extract_chain and chain.get_id() != extract_chain:
continue
structure_builder.init_seg(' ')
structure_builder.init_chain(chain.get_id())
resdict = {}
if res_renumber_flag:
# first_res = res_range_tuple[0]
# last_res = res_range_tuple[1]
resdict['before'] = select_residues_from_chain(
chain, first_res=first_res, gap_count=gap_count)
resdict['hit'] = select_residues_from_chain(
chain, first_res=first_res, last_res=last_res)
resdict['after'] = select_residues_from_chain(
chain, last_res=last_res, gap_count=gap_count)
else:
resdict['before'] = []
resdict['hit'] = chain.get_list()
resdict['after'] = []
new_resseq = start_resseq_by_default - len(resdict['before'])
resdict['water'] = chain_water_id(chain, water_id)
for key in ['before', 'hit', 'after', 'water']:
for residue in resdict[key]:
if res_renumber_flag:
new_resid = ' ', new_resseq, ' '
else:
new_resid = residue.get_id()
structure_builder.init_residue(residue.get_resname(),
*new_resid)
residue_atoms = None
if key == 'before':
residue_atoms = [atom for atom in residue if \
(atom.get_name() == 'C' or atom.get_name() == 'O')]
elif key == 'hit' or key == 'water':
residue_atoms = residue.get_list()
elif key == 'after':
residue_atoms = [atom for atom in residue if \
(atom.get_name() == 'N' or atom.get_name() == 'HN')]
for atom in residue_atoms:
structure_builder.init_atom(atom.get_name(),
atom.get_coord(),
atom.get_bfactor(),
atom.get_occupancy(),
atom.get_altloc(),
atom.get_fullname())
structure_builder.set_line_counter(line_counter)
line_counter += 1
new_resseq += 1
if key == 'water' and gap_count and len(
resdict['after']) != gap_count:
new_resseq += gap_count - len(resdict['after'])
out_structure = structure_builder.get_structure()
return out_structure
def read_PIC(
file: TextIO,
verbose: bool = False,
quick: bool = False,
defaults: bool = False,
) -> Structure:
"""Load Protein Internal Coordinate (.pic) data from file.
PIC file format:
- comment lines start with #
- (optional) PDB HEADER record
- idcode and deposition date recommended but optional
- deposition date in PDB format or as changed by Biopython
- (optional) PDB TITLE record
- repeat:
- Biopython Residue Full ID - sets residue IDs of returned structure
- (optional) PDB N, CA, C ATOM records for chain start
- (optional) PIC Hedra records for residue
- (optional) PIC Dihedra records for residue
- (optional) BFAC records listing AtomKeys and b-factors
An improvement would define relative positions for HOH (water) entries.
Defaults will be supplied for any value if defaults=True. Default values
are supplied in ic_data.py, but structures degrade quickly with any
deviation from true coordinates. Experiment with
:data:`Bio.PDB.internal_coords.IC_Residue.pic_flags` options to
:func:`write_PIC` to verify this.
N.B. dihedron (i-1)C-N-CA-CB is ignored in assembly if O exists.
C-beta is by default placed using O-C-CA-CB, but O is missing
in some PDB file residues, which means the sidechain cannot be
placed. The alternate CB path (i-1)C-N-CA-CB is provided to
circumvent this, but if this is needed then it must be adjusted in
conjunction with PHI ((i-1)C-N-CA-C) as they overlap (see :meth:`.bond_set`
and :meth:`.bond_rotate` to handle this automatically).
:param Bio.File file: :func:`.as_handle` file name or handle
:param bool verbose: complain when lines not as expected
:param bool quick: don't check residues for all dihedra (no default values)
:param bool defaults: create di/hedra as needed from reference database.
Amide proton created if 'H' is in IC_Residue.accept_atoms
:returns: Biopython Structure object, Residues with .internal_coord
attributes but no coordinates except for chain start N, CA, C atoms if
supplied, **OR** None on parse fail (silent unless verbose=True)
"""
proton = "H" in IC_Residue.accept_atoms
pdb_hdr_re = re.compile(
r"^HEADER\s{4}(?P<cf>.{1,40})"
r"(?:\s+(?P<dd>\d\d\d\d-\d\d-\d\d|\d\d-\w\w\w-\d\d))?"
r"(?:\s+(?P<id>[0-9A-Z]{4}))?\s*$")
pdb_ttl_re = re.compile(r"^TITLE\s{5}(?P<ttl>.+)\s*$")
biop_id_re = re.compile(r"^\('(?P<pid>[^\s]*)',\s(?P<mdl>\d+),\s"
r"'(?P<chn>\s|\w)',\s\('(?P<het>\s|[\w\s-]+)"
r"',\s(?P<pos>-?\d+),\s'(?P<icode>\s|\w)'\)\)"
r"\s+(?P<res>[\w]{1,3})"
r"(\s\[(?P<segid>[a-zA-z\s]+)\])?"
r"\s*$")
pdb_atm_re = re.compile(r"^ATOM\s\s(?:\s*(?P<ser>\d+))\s(?P<atm>[\w\s]{4})"
r"(?P<alc>\w|\s)(?P<res>[\w]{3})\s(?P<chn>.)"
r"(?P<pos>[\s\-\d]{4})(?P<icode>[A-Za-z\s])\s\s\s"
r"(?P<x>[\s\-\d\.]{8})(?P<y>[\s\-\d\.]{8})"
r"(?P<z>[\s\-\d\.]{8})(?P<occ>[\s\d\.]{6})"
r"(?P<tfac>[\s\d\.]{6})\s{6}"
r"(?P<segid>[a-zA-z\s]{4})(?P<elm>.{2})"
r"(?P<chg>.{2})?\s*$")
bfac_re = re.compile(r"^BFAC:\s([^\s]+\s+[\-\d\.]+)"
r"\s*([^\s]+\s+[\-\d\.]+)?"
r"\s*([^\s]+\s+[\-\d\.]+)?"
r"\s*([^\s]+\s+[\-\d\.]+)?"
r"\s*([^\s]+\s+[\-\d\.]+)?")
bfac2_re = re.compile(r"([^\s]+)\s+([\-\d\.]+)")
struct_builder = StructureBuilder()
# init empty header dict
# - could use to parse HEADER and TITLE lines except
# deposition_date format changed from original PDB header
header_dict = _parse_pdb_header_list([])
curr_SMCS = [None, None, None, None] # struct model chain seg
SMCS_init = [
struct_builder.init_structure,
struct_builder.init_model,
struct_builder.init_chain,
struct_builder.init_seg,
]
sb_res = None
rkl = None
sb_chain = None
sbcic = None
sbric = None
akc = {}
hl12 = {}
ha = {}
hl23 = {}
da = {}
bfacs = {}
orphan_aks = set() # []
tr = [] # this residue
pr = [] # previous residue
def akcache(akstr: str) -> AtomKey:
"""Maintain dictionary of AtomKeys seen while reading this PIC file."""
# akstr: full AtomKey string read from .pic file, includes residue info
try:
return akc[akstr]
except (KeyError):
ak = akc[akstr] = AtomKey(akstr)
return ak
def link_residues(ppr: List[Residue], pr: List[Residue]) -> None:
"""Set next and prev links between i-1 and i-2 residues."""
for p_r in pr:
pric = p_r.internal_coord
for p_p_r in ppr:
ppric = p_p_r.internal_coord
if p_r.id[0] == " ": # not heteroatoms
if pric not in ppric.rnext:
ppric.rnext.append(pric)
if p_p_r.id[0] == " ":
if ppric not in pric.rprev:
pric.rprev.append(ppric)
def process_hedron(
a1: str,
a2: str,
a3: str,
l12: str,
ang: str,
l23: str,
ric: IC_Residue,
) -> Tuple:
"""Create Hedron on current (sbcic) Chain.internal_coord."""
ek = (akcache(a1), akcache(a2), akcache(a3))
atmNdx = AtomKey.fields.atm
accpt = IC_Residue.accept_atoms
if not all(ek[i].akl[atmNdx] in accpt for i in range(3)):
return
hl12[ek] = float(l12)
ha[ek] = float(ang)
hl23[ek] = float(l23)
sbcic.hedra[ek] = ric.hedra[ek] = h = Hedron(ek)
h.cic = sbcic
ak_add(ek, ric)
return ek
def default_hedron(ek: Tuple, ric: IC_Residue) -> None:
"""Create Hedron based on same rdh_class hedra in ref database.
Adds Hedron to current Chain.internal_coord, see ic_data for default
values and reference database source.
"""
aks = []
hkey = None
atmNdx = AtomKey.fields.atm
resNdx = AtomKey.fields.resname
resPos = AtomKey.fields.respos
aks = [ek[i].akl for i in range(3)]
atpl = tuple([aks[i][atmNdx] for i in range(3)])
res = aks[0][resNdx]
if (aks[0][resPos] !=
aks[2][resPos] # hedra crosses amide bond so not reversed
or atpl == ("N", "CA", "C") # or chain start tau
or
atpl in ic_data_backbone # or found forward hedron in ic_data
or
(res not in ["A", "G"] and atpl in ic_data_sidechains[res])):
hkey = ek
rhcl = [aks[i][resNdx] + aks[i][atmNdx] for i in range(3)]
try:
dflts = hedra_defaults["".join(rhcl)][0]
except KeyError:
if aks[0][resPos] == aks[1][resPos]:
rhcl = [aks[i][resNdx] + aks[i][atmNdx] for i in range(2)]
rhc = "".join(rhcl) + "X" + aks[2][atmNdx]
else:
rhcl = [
aks[i][resNdx] + aks[i][atmNdx] for i in range(1, 3)
]
rhc = "X" + aks[0][atmNdx] + "".join(rhcl)
dflts = hedra_defaults[rhc][0]
else:
# must be reversed or fail
hkey = ek[::-1]
rhcl = [aks[i][resNdx] + aks[i][atmNdx] for i in range(2, -1, -1)]
dflts = hedra_defaults["".join(rhcl)][0]
process_hedron(
str(hkey[0]),
str(hkey[1]),
str(hkey[2]),
dflts[0],
dflts[1],
dflts[2],
ric,
)
if verbose:
print(f" default for {ek}")
def hedra_check(dk: str, ric: IC_Residue) -> None:
"""Confirm both hedra present for dihedron key, use default if set."""
if dk[0:3] not in sbcic.hedra and dk[2::-1] not in sbcic.hedra:
if defaults:
default_hedron(dk[0:3], ric)
else:
print(f"{dk} missing h1")
if dk[1:4] not in sbcic.hedra and dk[3:0:-1] not in sbcic.hedra:
if defaults:
default_hedron(dk[1:4], ric)
else:
print(f"{dk} missing h2")
def process_dihedron(a1: str, a2: str, a3: str, a4: str, dangle: str,
ric: IC_Residue) -> Set:
"""Create Dihedron on current Chain.internal_coord."""
ek = (
akcache(a1),
akcache(a2),
akcache(a3),
akcache(a4),
)
atmNdx = AtomKey.fields.atm
accpt = IC_Residue.accept_atoms
if not all(ek[i].akl[atmNdx] in accpt for i in range(4)):
return
da[ek] = float(dangle)
sbcic.dihedra[ek] = ric.dihedra[ek] = d = Dihedron(ek)
d.cic = sbcic
if not quick:
hedra_check(ek, ric)
ak_add(ek, ric)
return ek
def default_dihedron(ek: List, ric: IC_Residue) -> None:
"""Create Dihedron based on same residue class dihedra in ref database.
Adds Dihedron to current Chain.internal_coord, see ic_data for default
values and reference database source.
"""
atmNdx = AtomKey.fields.atm
resNdx = AtomKey.fields.resname
resPos = AtomKey.fields.respos
rdclass = ""
dclass = ""
for ak in ek:
dclass += ak.akl[atmNdx]
rdclass += ak.akl[resNdx] + ak.akl[atmNdx]
if dclass == "NCACN":
rdclass = rdclass[0:7] + "XN"
elif dclass == "CACNCA":
rdclass = "XCAXC" + rdclass[5:]
elif dclass == "CNCAC":
rdclass = "XC" + rdclass[2:]
if rdclass in dihedra_primary_defaults:
process_dihedron(
str(ek[0]),
str(ek[1]),
str(ek[2]),
str(ek[3]),
dihedra_primary_defaults[rdclass][0],
ric,
)
if verbose:
print(f" default for {ek}")
elif rdclass in dihedra_secondary_defaults:
primAngle, offset = dihedra_secondary_defaults[rdclass]
rname = ek[2].akl[resNdx]
rnum = int(ek[2].akl[resPos])
paKey = None
if primAngle == ("N", "CA", "C", "N") and ek[0].ric.rnext != []:
paKey = [
AtomKey((rnum, None, rname, primAngle[x], None, None))
for x in range(3)
]
rnext = ek[0].ric.rnext
paKey.append(
AtomKey((
rnext[0].rbase[0],
None,
rnext[0].rbase[2],
"N",
None,
None,
)))
paKey = tuple(paKey)
elif primAngle == ("CA", "C", "N", "CA"):
prname = pr.akl[0][resNdx]
prnum = pr.akl[0][resPos]
paKey = [
AtomKey(prnum, None, prname, primAngle[x], None, None)
for x in range(0, 2)
]
paKey.add([
AtomKey((rnum, None, rname, primAngle[x], None, None))
for x in range(2, 4)
])
paKey = tuple(paKey)
else:
paKey = tuple(
AtomKey((rnum, None, rname, atm, None, None))
for atm in primAngle)
if paKey in da:
process_dihedron(
str(ek[0]),
str(ek[1]),
str(ek[2]),
str(ek[3]),
da[paKey] + dihedra_secondary_defaults[rdclass][1],
ric,
)
if verbose:
print(f" secondary default for {ek}")
elif rdclass in dihedra_secondary_xoxt_defaults:
if primAngle == ("C", "N", "CA", "C"): # primary for alt cb
# no way to trigger alt cb with default=True
# because will generate default N-CA-C-O
prname = pr.akl[0][resNdx]
prnum = pr.akl[0][resPos]
paKey = [
AtomKey(prnum, None, prname, primAngle[0], None, None)
]
paKey.add([
AtomKey((rnum, None, rname, primAngle[x], None, None))
for x in range(1, 4)
])
paKey = tuple(paKey)
else:
primAngle, offset = dihedra_secondary_xoxt_defaults[
rdclass]
rname = ek[2].akl[resNdx]
rnum = int(ek[2].akl[resPos])
paKey = tuple(
AtomKey((rnum, None, rname, atm, None, None))
for atm in primAngle)
if paKey in da:
process_dihedron(
str(ek[0]),
str(ek[1]),
str(ek[2]),
str(ek[3]),
da[paKey] + offset,
ric,
)
if verbose:
print(f" oxt default for {ek}")
else:
print(f"missing primary angle {paKey} {primAngle} to "
f"generate {rnum}{rname} {rdclass}")
else:
print(
f"missing {ek} -> {rdclass} ({dclass}) not found in primary or"
" secondary defaults")
def dihedra_check(ric: IC_Residue) -> None:
"""Look for required dihedra in residue, generate defaults if set."""
# rnext should be set
def ake_recurse(akList: List) -> List:
"""Bulid combinatorics of AtomKey lists."""
car = akList[0]
if len(akList) > 1:
retList = []
for ak in car:
cdr = akList[1:]
rslt = ake_recurse(cdr)
for r in rslt:
r.insert(0, ak)
retList.append(r)
return retList
else:
if len(car) == 1:
return [list(car)]
else:
retList = [[ak] for ak in car]
return retList
def ak_expand(eLst: List) -> List:
"""Expand AtomKey list with altlocs, all combinatorics."""
retList = []
for edron in eLst:
newList = []
for ak in edron:
rslt = ak.ric.split_akl([ak])
rlst = [r[0] for r in rslt]
if rlst != []:
newList.append(rlst)
else:
newList.append([ak])
rslt = ake_recurse(newList)
for r in rslt:
retList.append(r)
return retList
# dihedra_check processing starts here
# generate the list of dihedra this residue should have
chkLst = []
sN, sCA, sC = AtomKey(ric, "N"), AtomKey(ric, "CA"), AtomKey(ric, "C")
sO, sCB, sH = AtomKey(ric, "O"), AtomKey(ric, "CB"), AtomKey(ric, "H")
if ric.rnext != []:
for rn in ric.rnext:
nN, nCA, nC = (
AtomKey(rn, "N"),
AtomKey(rn, "CA"),
AtomKey(rn, "C"),
)
# intermediate residue, need psi, phi, omg
chkLst.append((sN, sCA, sC, nN)) # psi
chkLst.append((sCA, sC, nN, nCA)) # omg i+1
chkLst.append((sC, nN, nCA, nC)) # phi i+1
else:
chkLst.append((sN, sCA, sC, AtomKey(ric, "OXT"))) # psi
rn = "(no rnext)"
chkLst.append((sN, sCA, sC, sO)) # locate backbone O
if ric.lc != "G":
chkLst.append((sO, sC, sCA, sCB)) # locate CB
if ric.rprev != [] and ric.lc != "P" and proton:
chkLst.append((sC, sCA, sN, sH)) # amide proton
try:
for edron in ic_data_sidechains[ric.lc]:
if len(edron) > 3: # dihedra only
if all(not atm[0] == "H" for atm in edron):
akl = [AtomKey(ric, atm) for atm in edron[0:4]]
chkLst.append(akl)
except KeyError:
pass
# now compare generated list to ric.dihedra, get defaults if set.
chkLst = ak_expand(chkLst)
altloc_ndx = AtomKey.fields.altloc
for dk in chkLst:
if tuple(dk) in ric.dihedra:
pass
elif sH in dk:
pass # ignore missing hydrogens
elif all(atm.akl[altloc_ndx] is None for atm in dk):
if defaults:
default_dihedron(dk, ric)
else:
if verbose:
print(f"{ric}-{rn} missing {dk}")
else:
# print(f"skip {ek}")
pass # ignore missing combinatoric of altloc atoms
# need more here?
def ak_add(ek: set, ric: IC_Residue) -> None:
"""Allocate edron key AtomKeys to current residue as appropriate.
A hedron or dihedron may span a backbone amide bond, this routine
allocates atoms in the (h/di)edron to the ric residue or saves them
for a residue yet to be processed.
:param set ek: AtomKeys in edron
:param IC_Residue ric: current residue to assign AtomKeys to
"""
res = ric.residue
reskl = (
str(res.id[1]),
(None if res.id[2] == " " else res.id[2]),
ric.lc,
)
for ak in ek:
if ak.ric is None:
sbcic.akset.add(ak)
if ak.akl[0:3] == reskl:
ak.ric = ric
ric.ak_set.add(ak)
else:
orphan_aks.add(ak)
def finish_chain() -> None:
"""Do last rnext, rprev links and process chain edra data."""
link_residues(pr, tr)
# check/confirm completeness
if not quick:
for r in pr:
dihedra_check(r.internal_coord)
for r in tr:
dihedra_check(r.internal_coord)
if ha != {}:
sha = {k: ha[k] for k in sorted(ha)}
shl12 = {k: hl12[k] for k in sorted(hl12)}
shl23 = {k: hl23[k] for k in sorted(hl23)}
sbcic._hedraDict2chain(shl12, sha, shl23, da, bfacs)
# read_PIC processing starts here:
with as_handle(file, mode="r") as handle:
for line in handle.readlines():
if line.startswith("#"):
pass # skip comment lines
elif line.startswith("HEADER "):
m = pdb_hdr_re.match(line)
if m:
header_dict["head"] = m.group("cf") # classification
header_dict["idcode"] = m.group("id")
header_dict["deposition_date"] = m.group("dd")
elif verbose:
print("Reading pic file", file, "HEADER parse fail: ",
line)
elif line.startswith("TITLE "):
m = pdb_ttl_re.match(line)
if m:
header_dict["name"] = m.group("ttl").strip()
# print('TTL: ', m.group('ttl').strip())
elif verbose:
print("Reading pic file", file, "TITLE parse fail:, ",
line)
elif line.startswith("("): # Biopython ID line for Residue
m = biop_id_re.match(line)
if m:
# check SMCS = Structure, Model, Chain, SegID
segid = m.group(9)
if segid is None:
segid = " "
this_SMCS = [
m.group(1),
int(m.group(2)),
m.group(3),
segid,
]
if curr_SMCS != this_SMCS:
if curr_SMCS[:3] != this_SMCS[:3] and ha != {}:
# chain change so process current chain data
finish_chain()
akc = {} # atomkey cache, used by akcache()
hl12 = {} # hedra key -> len12
ha = {} # -> hedra angle
hl23 = {} # -> len23
da = {} # dihedra key -> angle value
bfacs = {} # atomkey string -> b-factor
# init new Biopython SMCS level as needed
for i in range(4):
if curr_SMCS[i] != this_SMCS[i]:
SMCS_init[i](this_SMCS[i])
curr_SMCS[i] = this_SMCS[i]
if i == 0:
# 0 = init structure so add header
struct_builder.set_header(header_dict)
elif i == 1:
# new model means new chain and new segid
curr_SMCS[2] = curr_SMCS[3] = None
elif i == 2:
# new chain so init internal_coord
sb_chain = struct_builder.chain
sbcic = sb_chain.internal_coord = IC_Chain(
sb_chain)
struct_builder.init_residue(
m.group("res"),
m.group("het"),
int(m.group("pos")),
m.group("icode"),
)
sb_res = struct_builder.residue
if sb_res.id[0] != " ": # skip hetatm
continue
if 2 == sb_res.is_disordered():
for r in sb_res.child_dict.values():
if not r.internal_coord:
sb_res = r
break
# added to disordered res
tr.append(sb_res)
else:
# new res so fix up previous residue as feasible
link_residues(pr, tr)
if not quick:
for r in pr:
# create di/hedra if default for residue i-1
# just linked
dihedra_check(r.internal_coord)
pr = tr
tr = [sb_res]
sbric = sb_res.internal_coord = IC_Residue(
sb_res) # no atoms so no rak
sbric.cic = sbcic
rkl = (
str(sb_res.id[1]),
(None if sb_res.id[2] == " " else sb_res.id[2]),
sbric.lc,
)
sbcic.ordered_aa_ic_list.append(sbric)
# update AtomKeys w/o IC_Residue references, in case
# chain ends before di/hedra sees them (2XHE test case)
for ak in orphan_aks:
if ak.akl[0:3] == rkl:
ak.ric = sbric
sbric.ak_set.add(ak)
# may need altoc support here
orphan_aks = set(
filter(lambda ak: ak.ric is None, orphan_aks))
else:
if verbose:
print(
"Reading pic file",
file,
"residue ID parse fail: ",
line,
)
return None
elif line.startswith("ATOM "):
m = pdb_atm_re.match(line)
if m:
if sb_res is None:
# ATOM without res spec already loaded, not a pic file
if verbose:
print(
"Reading pic file",
file,
"ATOM without residue configured:, ",
line,
)
return None
if sb_res.resname != m.group("res") or sb_res.id[1] != int(
m.group("pos")):
if verbose:
print(
"Reading pic file",
file,
"ATOM not in configured residue (",
sb_res.resname,
str(sb_res.id),
"):",
line,
)
return None
coord = numpy.array(
(
float(m.group("x")),
float(m.group("y")),
float(m.group("z")),
),
"f",
)
struct_builder.init_atom(
m.group("atm").strip(),
coord,
float(m.group("tfac")),
float(m.group("occ")),
m.group("alc"),
m.group("atm"),
int(m.group("ser")),
m.group("elm").strip(),
)
# reset because prev does not link to this residue
# (chainBreak)
pr = []
elif line.startswith("BFAC: "):
m = bfac_re.match(line)
if m:
for bfac_pair in m.groups():
if bfac_pair is not None:
m2 = bfac2_re.match(bfac_pair)
bfacs[m2.group(1)] = float(m2.group(2))
# else:
# print f"Reading pic file {file} B-factor fail: {line}"
else:
m = Edron.edron_re.match(line)
if m and sb_res is not None:
if m["a4"] is None:
process_hedron(
m["a1"],
m["a2"],
m["a3"],
m["len12"],
m["angle"],
m["len23"],
sb_res.internal_coord,
)
else:
process_dihedron(
m["a1"],
m["a2"],
m["a3"],
m["a4"],
float(m["dihedral"]),
sb_res.internal_coord,
)
elif m:
print(
"PIC file: ",
file,
" error: no residue info before reading (di/h)edron: ",
line,
)
return None
elif line.strip():
if verbose:
print(
"Reading PIC file",
file,
"parse fail on: .",
line,
".",
)
return None
# reached end of input
finish_chain()
# print(report_PIC(struct_builder.get_structure()))
return struct_builder.get_structure()
